Ghost in the Shinobi
by Pharaoh Dresden
Summary: Following the defeat of Kayaba, a glitch in the system imprisons Kirito to a long and dark existence. When freedom is in his grasp, he finds himself in the era of warriors who wield chakra.


Disclaimer: I do not own Naruto or Sword Art Online.

Chapter 1

* * *

The world around him flickered with an intense, fragmented light, the sky itself splitting atop him and Asuna. And suddenly, Kirito was smashed with a twisting claustrophobia.

As games go, Sword Art Online was a titan of tightly constructed code. Its internal systems worked faster than any human alive to solve issues before players realized them. Perhaps it was this that truly made Kabaya's ambition possible, Kirito thought as panic began setting in.

Humans could only adapt so much. And for this game to become anywhere close to playable, the players would have had to start believing that this wasn't too far from reality. That the flesh on their bones was real before it evaporated into polygons. If glitches like warped colors and broken structures commonly associated with 3D and 2D games occurred regularly... That experience would quickly degenerate into a feeling of being truly trapped; where everything around them was nothing more than models generated by developers.

'We would have never made it to the top...' Kirito solemnly thought, his eyes widening at seeing the sky he once thought so similar to reality, bounce around. Its edges frayed like the fragile thing it was all along.

He tore his eyes from the sight, turning to watch Asuna, her skin flaking off her character model. Her virtual bones vibrated under her flesh disturbingly. He nearly stepped back but she grabbed his hand.

'Right, I probably look the same to her,' Kirito squeezed her hand back, hoping above all else that the game would release them in time. There must have been some delay between dying in the game and actually dying.

"Ki-r-ito #)(%#," he couldn't make out her words, but he nodded all the same, his eyes looking at where her eyes shined with unshed tears.

Before he could reply, the world fell into nothing. Not even darkness, no. The type of nothing a blind person would see.

He tried to speak, but nothing came out. He tried to move but he felt nothing. He tried to feel... but there were no emotions, only the fading sensation of Asuna's once warm hand.

'Am I dead? Is this death?'

...

'How long have I been here?'

...

'Who am I again?'

...

'?'

...

The ghost floated, its spirit bounded within a pinhole, never going beyond the small prison. But after so much time, too much to quantify, a hand touched the circuit. A hand that had previously been moving things around, scavenging for something useful. Perhaps it was this that caused the surge of static to jump from the skin into the seemingly dead circuitry.

Kirito's mind, long accustomed to the deadness that pervaded his being, began to pulse with alertness. The pulse was a feeling, the first in a long time. And then vision. Flecks of light flashed over, flying stars that opened his field of view with every coming second.

Then sound. A hum of what could only be life around him. It continued like this until he realized he was looking up at a blue sky, the same one he experienced with Asuna before the nothingness came.

Hesitantly, he sat up, patting his body and feeling the solidity of it. Tears dripped down his face, a huge relief filling him.

'I'm alive!' That nothingness, death, was something he never wanted to know again. It became a haunting loss of everything. The way it invaded his mind, leaving nothing for him to grasp as he battled with all his will. An unholy persistence to destroy every facet of Kazuto Kirigaya, Kirito, the Black Swordsman. A spark of panic lit in him and he trembled.

His hands squeezed so hard he half expected an HP ding.

'I need to stop panicking! Focus Kazuto!' He looked around, finding that he was where he and Asuna awaited their deaths earlier, standing in the sky and in front of an artificial sun.

But the emptiness beneath him troubled the newly awakened Kazuto.

'Where is Aincrad? Am I even on the server still?'

Kirito closed his eyes, his hands coming up to rub his forehead.

'I'm still in my avatar, so this isn't the real world, clearly. But... what the hell happened? If I'm still alive then why am I still here? It's impossible unless Kayabaya took his revenge out on me, leaving me trapped here as everyone else escaped into the real world.'

Groaning, he stood up, his legs shaking from the effort.

'But that doesn't make sense. The servers were going down. If I was still out there and hooked up to my NerveGear, then I would have just died. And if he really did secret me away to some separate server, Kayabaya wouldn't have left me like this. He's the type of guy to mess around with his victims... unless he died before he could.'

A nagging thought came to him. One that started small, but roared in his mind as the possibilities dwindled.

'My body is out there, but my mind, for all intents and purposes was hooked up to the NerveGear, transported into a virtual world. Could... maybe it was possible...'

He died. He knows he died. That eternal nothingness couldn't be anything but that, something he couldn't explain away.

'Maybe when you die you leave a little of your mind behind in the virtual world. But thousands died in SAO, why me?'

He remembered the falling sky and Asuna's distorted avatar.

'Am I a Ghost in a Machine? Is that even possible?'

Old memories, from when he first heard of NerveGear began to play back in his mind. Articles about the feasibility of memory transfers through VR tech. The movement of consciousness. Storage of the very soul.

'But could the SAO servers and tech really handle a brain's memories and consciousness?'

That bastard, Kayabaya... he wouldn't put it past the mass murderer. Kazuto clenched his fist, his eyes tearing up again. The drops fell, dissolving into particles as they landed on the sky floor.

A resignation filled him and he slowly opened his fist. For so long he had fought. First in Kayabaya's sick game and then within the nothingness of death. He was tired, too tired.

'Where do I even go... What do I even do in this empty place?'

...

Time had past for what was once the Black Swordsman. Time spent laying down or staring at the virtual sky that had started to become more opaque. The particle and color effects once lauded by virtual gamers everywhere losing complexity from a lack of power.

He had since given up escaping. No amount of effort uncovered a way out. He was just a series of 0s and 1s waiting to degrade with time just like the rest of this place. Most likely he would begin to lose this fake body and then his memories would start to crumble.

It was a terrifying thought. Sometimes he yearned that he could end it all, but even that was beyond his reach, limited as he was in this world.

Kazuto didn't think he had any more strength in him. Soon, he would fade completely away. And Suguha, his aunt and uncle, they would never see him again. Asuna... he would never explore what they had together.

A deep loathing filled him. Of VR, of NerveGear, of Kayabaya. Of this damn world. A loathing only intensified with time.

'I'm never leaving here.'

...

When he heard the hum a gasp escaped his mouth. It had been so long, too long since he heard sound. The power of this world was nearly exhausted, leaving only his body, still but tangible within a dark world.

Slowly, but surely, the world began to color. Light streamed down from the blue sky on a platform of air.

Kazuto blinked a few times and looked at his hands.

'...How? It's been so long, I thought no one would ever find me.'

He stood up shakily, his feet moving as if unsure and rusty.

Suddenly, he was hit with a nauseating feeling; A large shift in his awareness that became apparent instantly.

'Is... someone else here?' Kazuto spun around, searching for the presence he felt so keenly.

"..."

The Kirigaya's ears twitched. Something... something was speaking?

"...Kabuto it seems you've been invested in that little device for quite some time now, enough to connect it directly to the electric supply and mainframe. What secrets have you devoured from it?"

"Lord Orochimaru- I did not notice your arrival. My deepest apologies-"

"Enough. Now… what is so important about this piece of machinery? If I recall correctly, this was brought in some months ago from the northern coast," the man mused, and Kazuto finally registered his shock at hearing human voices in what felt like eternity.

"Hello! Can you hear me!? Hello!"

Kazuto's roars went unanswered as the men continued their conversation, a strange layer of static swaying in and out of their voices.

"... I see. The carbon dating readings seem preposterous, yet it wouldn't be impossible for humans to have developed metal based communication devices so long ago. There have ebbs and flows of civilization."

Kazuto continued screaming to no avail. As the minutes went by, he finally started to calm down; enough to catch the tail end of their conversation.

"A miniaturized cell processor attached to a local drive? Intriguing. That and the fact that it seems to be on a low power output strikes me as something worth studying. It's a shame you have not been able to get through the encrypted memory," the man seemed to pause there.

"Be sure to secure your connections. This technology may as well be alien and our firewalls may not hold," at that the voices went silent.

Kazuto looked blankly upwards, infuriated he could not make his voice heard but confused as he ran back the conversation in his head.

"... They think I'm some kind of processor... Could it be that I really am a Ghost in the Machine?" Kazuto rasped, his voice tinged with hysteria in the face of knowing the actual truth.

He did not move for several minutes, his hands shaking and eyes stuck to a glint of light in the distance.

"Wait... they said I was connected to their computers. If I can slip through to their side I can make contact!" It would explain how he could hear them. The built in plug and play bus that was most likely connected with the processor must have allowed him to use their own microphones to listen in on the men speaking.

A shiver of hope crawled up his back. It wasn't too late. He could contact the outside world, get help, return to his body.

'If my body is still alive...' The thought came instantly, but he ignored it, burying it deep inside. He didn't have time for panic.

He sat down and closed his eyes.

'I need to find this connection. If I really am an avatar, a consciousness given form in this world. Then like Yui, I must have some kind of access, as small as it is, with the system settings.'

Kazuto tried for several hours, moving his fingers to access his menu, but failed to generate some kind of response.

"..."

He sighed and laid down. His eyes watched the blue sky. Never did he find it so tedious as he did in that moment.

"I need to wait for them to attempt to decrypt the drive. Maybe something'll happen then. The system could restart in an attempt to block the attacker and that would by my chance to access the command line," he murmured. He had plenty of experience waiting, but he had a feeling this would be the hardest yet.

...

When it came it was obvious. The presence grew around him like a hum of electricity and as he predicted, everything went dark. The power flickered slightly before slowly turning back on. Kazuto immediately focused and flicked his hand down in the traditional menu access gesture.

The appearance of a white pane was a rush of fire in his veins. As quickly as possible he went through the items until he found what he was looking for.

'Troubleshoot!' A quick tap took him to a series of options written with a font slightly more archaic than the previous options. He found the command prompt relatively easily.

'Now... what was it...' He had been so focused on getting access to the command prompt that he hadn't planned for when he actually got it.

Kazuto narrowed his eyes. He just needed to see all available directories. If he was right, the external connection would just display as another letter drive. Then he'd have to transfer a piece of his memory that controlled the rest into the external system.

'Just have to be careful to leave the bulk of my consciousness back here. I doubt these guys have the architecture to handle it.' With an impressive typing speed he navigated to the necessary directories and browsed for something that looked like it would interface with his consciousness.

A program with the extension .ng was in the list of thousands of other files.

'...Nervegear,' typing the move command, he hesitated for a few seconds before pressing enter.

'I don't care what happens as long as something changes.'

In a blur of his surroundings he appeared in the middle of a laboratory, unable to truly see anything.

'Wait... how did I know it was a lab?' The observation did not end there.

'...Elemental nations, jutsu, clan bloodlines,' what in the world was going on? Kazuto knew things he had never even heard of before. The stream of knowledge kept flowing into him and finally a sudden realization crept in.

'This is all too genuine, too thorough to be some work of fiction. But these things can't be true! This isn't some fantasy, it's real life!' A sense of panic took a hold of him, but it was overwhelmed as his senses expanded. His awareness grew, a river of consciousness flowing into the other pockets of connected computers scattered throughout the entire Sound Village base. As if it was a primitive version of the Internet.

Entire memory banks and information too complex to be made up attacked his mind in a flurry of data.

'...My consciousness, the .ng file... it must have adapted to the directories like it would my own memory. I... I assimilated it all,' Kazuto's thoughts trailed off, too busy handling the gigantic amount of information sweeping through him.

And then it hit. If he could widen his eyes, if he even had eyes, then they would be filled with an intense horror.

'Where in the hell am I!? Where is Japan, the US, everything else?' All that was left were countries he didn't recognize, a language he realized was slightly varied from Japanese but not the same.

'Is this the future?' Kazuto paused, his mind stretching as it finished absorbing everything else.

'Then... then everyone I knew...' Kazuto's words trailed off, a lifetime of experiences and emotions between pauses.

They were dead. Long gone. Not even ash at this point. No hint of their existence in this new world of his.

'D-did they die not knowing I was alive...?' Kazuto went cold, a chill of utter helplessness filling him.

Agil, Klein, Silica, Lisbeth, Yui, Suguha, Asuna... His aunt and uncle. He would never see them again. It was too cruel, too horrifying...

Kazuto dissolved into a stillness, blocking out all his thoughts and emotions. This pain, it would fade in time. But he needed to act now. He needed to be free from this machine, somehow.

The answer came involuntarily. Waves of keywords associated with images and experiments that made him gag.

Human puppets, tissue growth, curse seal soul implantation, human resurrection. The faded memories that he recalled were formed from documents, videos and pictures hosted on the servers he pilfered. Kazuto put a stop to it immediately, the nausea of such disgusting experiments proving to be too much.

'Monster... This Orochimaru can't be human,' he recoiled in horror. Just where did he land himself? Even now, as he recollected what little sanity he had left, he realized that the language he was thinking in had changed slightly.

'The .ng file must have adapted my language without me even noticing...' Kazuto blankly thought, the emotions he desperately kept at bay only hinting at the sorrow. He was just a teenager born in one of the most affluent countries in the world. Sword Art Online had been filled with its own share of brutality and player killers; an unthinkable scenario orchestrated by a madman. But this... this was too much for him.

Yet in the ocean of madness, he felt a sliver of a solution develop against his will.

'I can't be thinking of using Orochimaru's information...' the teenager's thoughts contradicted his actions, as several white panes appeared in the once dark void. His avatar glowed as light reflected off of it, the panes growing in size as directories opened up containing information he could barely stomach.

'...my consciousness could be mapped through a seal... embedded into brain tissue formed through samples,' Kazuto absently pondered.

The body would have to be created using significant amounts of tissue and organ generation. Lab AB had tubes filled with dead flesh from previous, failed experiments. That base component and the use of the chakra organ Orochimaru had developed years ago should allow him to design a seal following his commands.

Hundreds of connections broke and reformed themselves as Kazuto refined his solution, each connection bringing it closer to feasibility.

'The fundamental seal designs are already there. I just need to shape or "program" the body into my own image, rather than Orochimaru's,' the teen paused as he ruminated on the issue.

It would take several months to develop it. And it would be risky. But during the seal development, he could harness the computing power of the Orochimaru's base to establish plans to even enhance his body.

'Orochimaru isn't the only monster... the things these shinobi are capable of are in a way frightening. I'm not sure I should call people who could breathe fire or jump across football fields human. It even beats out Sword Art Online and that wasn't real...'

Though it may be the case this place wasn't even real. Perhaps he sunk deeper into virtual space, one level below Sword Art Online.

He ignored the confusing thought and moved on. It was too much to think about now.

'My body would need to be able to defend itself. But surprisingly...' There were no detailed records on jutsu. In fact, the only fully documented techniques were related to fuinjutsu.

'It seems Orochimaru was wary of his knowledge being stolen, specifically his ability to stay alive across several bodies,' a stiff smile appeared on his face. Orochimaru hadn't accounted for someone using the little that the Snake Sannin documented about fuinjutsu to recreate that ability. And just what he was going to use to transfer his consciousness, .ng file and all, directly into his prepared body with a cursed seal.

But the lack of techniques Kazuto could use would be a problem. A chakra system could be implemented with the tissue samples native to this land, but...

'I need to somehow make techniques using chakra, an incredible energy. Almost like an RPG's mana...But how?' The internal question sparked a litany of directories to open, the term "Chakra Mechanics" repeated multiple times in them.

'Chakra reinforcement, focusing, neural synapses...' Not much detail about elements or the strange Yin and Yang concepts, but Kazuto quickly caught on.

These mechanics described the use of simple chakra applications to the body, making for a physically powerful warrior. Super strength, speed, reaction-time, shielding other surfaces, all were viable with chakra. Even unleashing pure chakra in a shockwave type of attack.

'I could recreate SAO's sword techniques with these applications. But it looks like they're limited. Normal shinobi can't use these too often in succession because of a limited supply,' Kazuto sped through the notes Orochimaru left.

He could alter the chakra network in the tissue samples to grow in specific areas, enlarging and shrinking tenketsu to maximize the use of the chakra applications. His memory knew how to use the techniques, but he knew that VR was still too far from reality for that to be relevant.

Kazuto opened more directories and his lips twitched upwards.

'I just need to take advantage of the existing flesh's muscle memories. Maybe I can recreate the flow of chakra to map SAO techniques to mimic experiences...' Kazuto pondered, his thoughts straightening as he used the cameras in the base to watch Orochimaru and his assistants work.

The man looked as freakishly monstrous as he acted. A pale white face with purple markings indicative of a snake.

'As sly as one too.'

Some time would elapse before he could fully implement the plan, but it was nothing compared to everything he had experienced. His avatar's hands shook, a leak in the emotions boiling beneath the surface of his calm appearance.

His eyelids closed slightly, enough to only make out only specks of light where the panes floated.

'I need to make this work- or it'll be all for nothing. It'll- it'll be the end of this suffering. One way or another...'

Kazuto closed his eyes. Just a bit more time.

...

Seven Months Later

"Kabuto, what is this about a leak of poison gas in Lab AB?" He had seen the dead bodies and near dead crawling across the hallway towards that sector. The screams of agony had been an irritating distraction to his work.

"Orochimaru-sama, we are currently working on getting it under control. One of the exhaust vents had been damaged from some electrical problems. Unfortunately, the nature of the gas requires hazmat suits, which incidentally have been locked away in their storage unit by the very same electrical problems," Kabuto's clinical explanation gave way to curiosity near the end. And Orochimaru paused in thought.

"How convenient. Are the cameras in the lab incapacitated by these same 'electrical problems'?" Kabuto nodded casually in response.

Orochimaru folded his arms, tapping one finger methodically as his mind cycled through possibilities.

"It would be quite the scheme. To orchestrate these incidents to gain uninterrupted access to Lab AB," Kabuto posited and Orochimaru ignored the unnecessary comment.

The Snake Sannin slipped away, his form fading in the shadow of the room they were both in. Immediately he appeared from inside the lab's wall, his skin turning slightly purple as the fumes sunk inside the pores. Seconds later the same skin regained its unnatural, pale color.

Purple smoke concealed the room, the metal tables and tubes only fading in and out of sight as the smoke billowed.

In silence, the Sannin flickered to the ground. His gait was calm as he focused his ears to the surroundings, only electrical discharges catching his attention from above.

"Interesting..." Instantly, chakra flooded the room, blowing away the smoke and leaving the bloodied metal floors visible.

The Sannin ignored the messy sight and his keen eyes quickly found the broken tube, the glass cover shattered. As he studied the large hole in the middle of the glass, a sudden realization pierced him.

He peered at the floor, noticing how the glass was sprayed outwards from the point of impact. A white and yellow jelly-like substance was congealing at the bottom of it, blood surrounding the material; gallons of the red liquid had been steadily pouring out onto the lab floor.

"It was destroyed from the inside..." Orochimaru dipped a finger in the yellow-ish substance and flicked his tongue over it, only smiling at the sour taste.

He turned to face the side as Kabuto flickered next to him.

"Orochimaru-sama, jus-just what happened here?" Orochimaru chuckled at the hint of disgust beneath Kabuto's breath.

"It seems that something has escaped from the lab. Something that made full use of it before-" He smiled widely at the congealed mixture in the tube, "-it felt ready to leave."

Kabuto was speechless for a few seconds.

"How were they able to overload our circuit breakers? And as hard as it to believe, it is as if someone did this remotely, making full use of the maturation chemicals; though we were only barred from the room for a few hours." Orochimaru tilted his head to peer at his assistant, briefly pondering the observations.

"Salvage any recordings. And do make sure to punish the guards for a disappointing effort," Orochimaru took one last glance at the tube and turned around, walking away as his form slowly faded into the shadows of the room.

Kabuto adjusted his glasses, the fluorescent lights hitting them with a glare.

He would have to investigate thoroughly. These tubes were specifically made for human maturation experiments, but they were long abandoned after his master developed the Living Corpse Reincarnation technique. The maturation chemicals could create flesh and bones, generating a living body. But there had been the unfortunate side effect of cancerous growths; the programs encoding the DNA sequences not capable enough to map the genome properly.

And they hadn't even begun the next step involving the transfer of the soul.

If someone made use of them... Kabuto turned to glance around the room. Then perhaps that person had solved a problem they hadn't even been capable of thinking about yet.

With silent steps he made his way back to his own lab, ignoring the chill that went up his spine.

Kirito stumbled out of the underground base, his feet trembling and weak from disuse.

'Or is it no use at all?' With a grimace he pushed himself forward, worried that this escape route would be found despite all his planning.

'This is one of the fastest ways to escape, but it was also risky...' Kazuto had planned the route to the last inch and guard rotation, but he underestimated how weak he would be in this newly formed body.

He looked down at his fingers, their pruny, pale, but firm shape sending a shiver of joy up his spine.

'I still can't believe I was able to do that...' What were the chances the one place in the elemental nations where he could create a human body with his likeness was also the same place he was taken. It had been something he pondered heavily as he planned, his thoughts turning to VR.

'But I don't have time to think, I need to make it past the valley by at least 2 kilometers before the cameras come back online.'

With a burst of energy he picked up his pace, ignoring the wheeze of his own breath.

...

"Ha... Ha... I... barely... made it," the once black swordsman fell face down on the shrubbery in front of him; the plants itchy against his naked body.

His pants slowly dwindled into deep breaths, the sense of danger dissipating with each passing second. The forest around him was just beyond the valley and a few kilometers from the Sound Village. It was enough to avoid the sensory ninja currently in the village.

"J-just need to rest now so I can take off in an hour. Orochimaru won't be able to detect me this far away, but he'll have trackers on me soon..." Closing his eyes, Kazuto crossed his arms across his body and sunk deeper into the green plants. A small nap would do him some good.

Before his body could finally settle, a sharp crack sliced through the air, forcing him to jump awake on shaky legs. Bleary eyes focused and attempted to find the source of the sound.

"Tch..." Kazuto didn't see anything, though that meant little with ninja.

'I couldn't have been spotted...' With slow movements he backed up, watching carefully for anything behind the dark copse of trees.

Almost like a phantom, a black shadow flickered forward from behind the trees.

Kazuto barely caught the shadow's movements, his eyes still too unfocused in his new body. Though it became obvious he was in trouble when he immediately recognized who it was. Or rather who she was.

The Kunoichi was Tayuya, a Sound ninja specializing in genjutsu and assassinations. More importantly, she was one of Orochimaru's Sound Five. His throat suddenly felt impossibly drier.

"...Tsk, what shithole did you crawl out of?" The girl's red hair distracted him for a few seconds, causing her to glare even harder at him. She paid no attention to his naked form and modesty was the last thing on his mind now.

"You fucking deaf?" Kazuto gulped in response. One wrong word here and he'd be in Orochimaru's clutches again. He wasn't strong enough to escape a genin, let alone a high level fighter like Tayuya.

"S-sorry," immediately he began groveling. His body slouched forward, making his already withered and deathly skinny form appear more pathetic.

"I-I ran from my home, I-I coul-ldn't t-take it an- anymore," Kazuto inwardly grimaced at the ridiculous backstory. He silently apologized to his own family which was the polar opposite in this imaginary story.

Almost imperceptibly, Tayuya's glare softened, the sharp glint of her eyes becoming more neutral.

"Get lost kid, before Lord Orochimaru the Legendary Snake Sannin feeds on your corpse," with that she flickered away, her form disappearing into the twisting shadows.

In seconds he galloped away, his weak form barely staying upright but the fear pushing him to keep moving.

'Didn't realize any of his soldiers had an ounce of mercy.' With that last thought Kazuto made his way into the shadows of the trees ignoring every sense of exhaustion attacking him.

* * *

Author's Note:

Let me know your thoughts.


End file.
